I tend to use dependent clauses frequently in scientific writing. This is especially true when discussing a problem-solving process where the result from one step leads into the next. Here's a made-up example, with the dependent clauses in bold.

To overcome the issue of noise, we performed a Fast Fourier transform on the resultant time series. Although the output represented only half of the observations, we temporally interpolated the remaining observations based on historical trends archived previously. Moreover, the use of temporal interpolation allows us to fill data gaps when the detector failed to make observations.

When I try to integrate the dependent clause into the independent clause, the paragraph loses the logical flow of problem-then-solution sentence construction and the sentences feels disjointed:

We performed a Fast Fourier transform on the resultant time series to overcome the issue of noise. We temporally interpolated the remaining observations based on historical trends archived previously because the output represented only half of the observations. The use of temporal interpolation also allows us to fill data gaps when the detector failed to make observations.

While I do prefer the first version, is it stylistically and technically undesirable to use dependent clauses in successive sentences? Or am I just being paranoid?

Moving the dependent clause after the independent clause does not make the dependent clause into something else. It's still a dependent clause.
– phoogDec 14 '11 at 23:21

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Keep the first version. I don't know why you think there's anything wrong with it---it's much better. The second version puts the material in the wrong order and thus destroys the logical links between sentences, making it harder to understand. Using too many dependent clauses in scientific writing is a common mistake, but you are not anywhere close to doing that yet.
– Peter Shor Dec 15 '11 at 3:33

2 Answers
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As pointed out by @phoog - and you seem to be aware of this - the dependent clause (in your case these are adverbial clauses) can be at either the start or end of the sentence; it still remains a dependent clause. I would say the best place for the dependent clause is where it promotes readability and ease of comprehension of the sentence. In the examples you give above I generally find those with the dependent clause at the start more readable, particularly given the context of "problem-solution" as you say. This seems a sensible approach when you are indeed outlining in technical terms problems that you have overcome.

I can see no reason why either is more or less desirable than the other per se, whether it be in technical writing or prose. I would say that clarity should be foremost in any case. In practice, perhaps a mixture of both is the natural outcome, depending on the appropriate conceptual flow.

As Phoog says, your terminology is a bit off, but your style looks absolutely fine to me, though it is hard to tell without proper content (or content that I can understand). While very complex sentences may be be easier to follow if the main clause comes first, your sentences are readable enough. Your clauses and phrases that precede the main clause are not so long or complicated that they obscure the structure of the sentence.